Gut Analysis Toolbox enables semi-automated analysis of the neuronal and glial distribution within the gut wall (enteric nervous system). It uses a combination of FIJI macros
, StarDist, CLIJ
and deepImageJ for segmentation and analysis.
Click here to access the WIKI detailed instructions on how to use GAT.A detailed how to use instructions with wiki is available here:
You can also watch tutorials for GAT on Youtube.
What you can do with GAT:
- Semi-automated analysis of number of enteric neurons: Uses pan-neuronal marker Hu or anything with similar labelling
- Normalise counts to the number of ganglia.
- Count number of neuronal subtypes, such as ChAT, nNOS etc..
- Spatial analysis using number of neighboring cells.
- Calcium imaging analysis: Alignment of images and extraction of normalised traces
Reference
Software citation on Zenodo:
Luke Sorensen, Ayame Saito, Sabrina Poon, Myat Noe Han, Adam Humenick, Keith Mutunduwe, Christie Glennan, Narges Mahdavian, Simon JH Brookes, Rachel M McQuade, Jaime PP Foong, Sebastian K. King, Estibaliz Gómez-de-Mariscal, Robert Haase, Simona Carbone, Nicholas A. Veldhuis, Daniel P. Poole, & Pradeep Rajasekhar (2022). Gut Analysis Toolbox (1.0.0). Zenodo. doi: 10.5281/zenodo.6095590
To download the training data, notebooks and associated models please go to the following Zenodo link: